Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses

Abstract

Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.

Low Temperature Stress Tolerance: An Insight Into the Omics Approaches for Legume Crops

“…Many transcriptomic studies in A. thaliana have been undertaken in order to decipher cold responses (Bahrman et al, 2019). Some high throughput transcriptomic analyses have been performed in some legumes (Fabaceae), such as Vicia faba (Lyu et al, 2021), Pisum sativum (Bahrman et al, 2019), Arachis hypogaea (Jiang et al, 2020), Ammopiptanthus mongolicus (Pang et al, 2013), Glycine max (Kidokoro et al, 2015), Lotus japonicus (Calzadilla et al, 2016), Vigna unguiculata, subspecies sesquipedalis (Tan et al, 2016), Vigna subterranean (Bonthala et al, 2016), Medicago falcate (Miao et al, 2015), Medicago sativa (Song et al, 2016), and Cicer arietinum (Sharma and Nayyar, 2014). Transcriptomic studies in these legume species under the exposure of cold stress have led to altered transcript of genes (Buti et al, 2018;Guan et al, 2019).…”

Comparative Metabolomic and Transcriptomic Studies Reveal Key Metabolism Pathways Contributing to Freezing Tolerance Under Cold Stress in Kiwifruit

“…The fluidity of membrane composition plays an central role in temperature perception, which reduces to form a solid gel capable of sensing cold stress ( Gilad et al, 2018 ; Yang et al, 2019 ), while changes in the content of soluble sugars may play a key role in cold signaling transduction by regulating the expression of cold-responsive genes ( Krasensky and Jonak, 2012 ). Besides metabolomics, high-throughput sequencing techniques like transcriptomics have been widely used to explore the problem of coping with abiotic stress in a wide range of plants ( Bahrman et al, 2019 ). The ICE–CBF–COR regulation network response to cold stress was discovered using RNA-Seq technology, in which cold stress induces the expression of transcriptional factors, including AP2-domain protein CBFs, which activate the expression of various downstream cold responsive (COR) genes ( Stockinger et al, 1997 ; Wanqian et al, 2018 ).…”

Integrated sRNA-seq and RNA-seq Analyses Reveal a microRNA Regulation Network Involved in Cold Response in Pisum sativum L.

“…The transcriptomic responses of the two contrasted pea lines (Ch, frost tolerant; Te, frost susceptible) subjected to a cold acclimation treatment (4.5 °C; LT) or not (N) before applying frost was studied after different periods of cold exposure T1 and T2 [11]. For The transcriptomic responses of the two contrasted pea lines (Ch, frost tolerant; Te, frost susceptible) subjected to a cold acclimation treatment (4.5 • C; LT) or not (N) before applying frost was studied after different periods of cold exposure T1 and T2 [11]. For both periods, we identified four sets of DEGs: (1) between LT and N in Ch at T1 (Table S9);…”